{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "06576251",
   "metadata": {},
   "source": [
    "# Generate Protein Embeddings\n",
    "\n",
    "As an example, here's how to proccess the frog reference proteome with ESM1b.\n",
    "\n",
    "You can find proteome fastas on ENSEMBL: https://uswest.ensembl.org/info/data/ftp/index.html\n",
    "\n",
    "We use a pretrained Transformer model from https://github.com/facebookresearch/esm. These models were trained on hundreds of millions of protein sequences from across the tree of life.\n",
    "\n",
    "**NOTE:** These protein embedding scripts require an older version of the ESM Repo: you should checkout commit:\n",
    "[`839c5b82c6cd9e18baa7a88dcbed3bd4b6d48e47`](https://github.com/facebookresearch/esm/commit/839c5b82c6cd9e18baa7a88dcbed3bd4b6d48e47)\n",
    "\n",
    "**Clone the ESM repo.**"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2d9f1222",
   "metadata": {},
   "source": [
    "## Step 1: Download reference proteome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "6ef60cf4",
   "metadata": {},
   "outputs": [],
   "source": [
    "!mkdir data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "id": "0280ef79",
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "NAME = \"Xenopus_tropicalis.UCB_Xtro_10.0.pep.all\" # CHANGE THIS TO THE NAME OF THE REFERENCE PROTEOME YOU WANT\n",
    "DATA_PATH = os.path.abspath(os.getcwd()) + \"/data\" # PATH TO DATA DIRECTORY (YOU CAN USE THE ONE IN THIS DIRECTORY)\n",
    "ESM_PATH = \"/lfs/local/0/yanay/esm/\" # MAKE SURE TO CHANGE THIS TO THE PATH YOU CLONED THE ESM REPO TO ESM PATH\n",
    "TORCH_HOME = \"/dfs/project/cross-species/yanay/torch_home\" # MAKE SURE TO CHANGE THIS TO YOUR DESIRED DIRECTORY\n",
    "DEVICE=6 # GPU NUMBER, CHANGE THIS\n",
    "\n",
    "# PATH TO ENSMBL PROTEOME FASTA, CHANGE THIS\n",
    "FASTA_URL = \"https://ftp.ensembl.org/pub/release-108/fasta/xenopus_tropicalis/pep/Xenopus_tropicalis.UCB_Xtro_10.0.pep.all.fa.gz\" "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "id": "b7af32df",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "WARNING: combining -O with -r or -p will mean that all downloaded content\n",
      "will be placed in the single file you specified.\n",
      "\n",
      "--2022-11-14 15:30:40--  https://ftp.ensembl.org/pub/release-108/fasta/xenopus_tropicalis/pep/Xenopus_tropicalis.UCB_Xtro_10.0.pep.all.fa.gz\n",
      "Resolving ftp.ensembl.org (ftp.ensembl.org)... 193.62.193.139\n",
      "Connecting to ftp.ensembl.org (ftp.ensembl.org)|193.62.193.139|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 11316909 (11M) [application/x-gzip]\n",
      "Saving to: ‘data/Xenopus_tropicalis.UCB_Xtro_10.0.pep.all.fa.gz’\n",
      "\n",
      "data/Xenopus_tropic 100%[===================>]  10.79M   430KB/s    in 26s     \n",
      "\n",
      "2022-11-14 15:31:06 (429 KB/s) - ‘data/Xenopus_tropicalis.UCB_Xtro_10.0.pep.all.fa.gz’ saved [11316909/11316909]\n",
      "\n",
      "FINISHED --2022-11-14 15:31:06--\n",
      "Total wall clock time: 26s\n",
      "Downloaded: 1 files, 11M in 26s (429 KB/s)\n"
     ]
    }
   ],
   "source": [
    "!wget -r {FASTA_URL} \\\n",
    "        -O data/{NAME}.fa.gz"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "id": "88da8618",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "gzip: data/Xenopus_tropicalis.UCB_Xtro_10.0.pep.all.fa already exists; do you wish to overwrite (y or n)? ^C\n"
     ]
    }
   ],
   "source": [
    "!gunzip data/{NAME}.fa.gz"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "04e037e9",
   "metadata": {},
   "source": [
    "## Step 2: Clean Fasta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "id": "c2913975",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of original sequences = 49,792\n",
      "100%|█████████████████████████████████| 49792/49792 [00:00<00:00, 146933.93it/s]\n",
      "Number of cleaned sequences = 49,792\n"
     ]
    }
   ],
   "source": [
    "!python clean_fasta.py \\\n",
    "--data_path=./data/{NAME}.fa \\\n",
    "--save_path=./data/{NAME}.clean.fa"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6d011546",
   "metadata": {},
   "source": [
    "## Step 3: Run ESM"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "id": "6a4fda90",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Transferred model to GPU\n",
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   "source": [
    "# THE MODELS ARE VERY LARGE AND TAKE A WHILE TO RUN\n",
    "\n",
    "!export TORCH_HOME={TORCH_HOME}; cd {ESM_PATH}/scripts/; \\\n",
    "CUDA_VISIBLE_DEVICES={DEVICE} python extract.py esm1b_t33_650M_UR50S \\\n",
    "{DATA_PATH}/{NAME}.clean.fa \\\n",
    "{DATA_PATH}/{NAME}.clean.fa_esm1b \\\n",
    "--include mean  --truncate"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "01247c6f",
   "metadata": {},
   "source": [
    "## Step 4: Convert to Embeddings File"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "id": "f6700efc",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "100%|█████████████████████████████████| 49792/49792 [00:00<00:00, 253804.51it/s]\n",
      "Number of gene symbols = 14,718\n",
      "Number of protein IDs = 39,310\n",
      "100%|███████████████████████████████████| 39310/39310 [00:21<00:00, 1834.55it/s]\n",
      "data/Xenopus_tropicalis.UCB_Xtro_10.0.pep.all.clean.fa_esm1b/ENSXETP00000100112.2.pt\n",
      "100%|██████████████████████████████████| 14718/14718 [00:00<00:00, 36799.51it/s]\n"
     ]
    }
   ],
   "source": [
    "!python map_gene_symbol_to_protein_ids.py \\\n",
    "    --fasta_path ./data/{NAME}.fa \\\n",
    "    --save_path ./data/{NAME}.gene_symbol_to_protein_ID.json\n",
    "\n",
    "\n",
    "!python convert_protein_embeddings_to_gene_embeddings.py \\\n",
    "    --embedding_dir ./data/{NAME}.clean.fa_esm1b \\\n",
    "    --gene_symbol_to_protein_ids_path ./data/{NAME}.gene_symbol_to_protein_ID.json \\\n",
    "    --embedding_model ESM1b \\\n",
    "    --save_path ./data/{NAME}.gene_symbol_to_embedding_ESM1b.pt\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fb28f620",
   "metadata": {},
   "source": [
    "## STEP 5: Running SPEAR"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "id": "8c9a7a44",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/dfs/project/cross-species/yanay/code/SPEAR/protein_embeddings/data/Xenopus_tropicalis.UCB_Xtro_10.0.pep.all.gene_symbol_to_embedding_ESM1b.pt'"
      ]
     },
     "execution_count": 50,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Your final embeddings will be located at: \n",
    "os.path.abspath(f\"./data/{NAME}.gene_symbol_to_embedding_ESM1b.pt\")"
   ]
  }
 ],
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